AMBER Archive (2006)

Subject: Re: AMBER: Gb Na+ ions DNA

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Fri Jul 21 2006 - 04:22:21 CDT

Hi,
> I have been trying to simulate a DNA chain and Na+ counterions (added using
> leap) by way of sander and the
> implicit GB approx.
> My problem is that on starting md to equilibrate the system the Na+ ions
> quickly fly away from the DNA chain.
> I have tried a couple of different protocols for equilibriation and
> minimisation to no avail.
> Is there some obvious reason why this is happening that I am overlooking?
...yes. It is rather easy to show that the (thermodynamic) average
distance between an ion and the solute is infinite. So what you see has
not only been observed by many (me included) but is also not unexpected.
One can try various things to change that (temporarily by somehow causing
stronger attachment between solute and ions) of "forever" by enclosing
both e.g. inside an elastic sphere. I guess both tricks won't lead to
new insights about molecules, but can be fun to implement :-)

good luck
Andreas

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